Job ID = 6368812 SRX = SRX5985666 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:40:07 prefetch.2.10.7: 1) Downloading 'SRR9214971'... 2020-06-16T00:40:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:12 prefetch.2.10.7: 1) 'SRR9214971' was downloaded successfully Read 19842184 spots for SRR9214971/SRR9214971.sra Written 19842184 spots for SRR9214971/SRR9214971.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:23 19842184 reads; of these: 19842184 (100.00%) were unpaired; of these: 8851127 (44.61%) aligned 0 times 9622325 (48.49%) aligned exactly 1 time 1368732 (6.90%) aligned >1 times 55.39% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1413083 / 10991057 = 0.1286 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:55:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:21: 1000000 INFO @ Tue, 16 Jun 2020 09:55:28: 2000000 INFO @ Tue, 16 Jun 2020 09:55:35: 3000000 INFO @ Tue, 16 Jun 2020 09:55:42: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:55:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:49: 5000000 INFO @ Tue, 16 Jun 2020 09:55:52: 1000000 INFO @ Tue, 16 Jun 2020 09:55:57: 6000000 INFO @ Tue, 16 Jun 2020 09:56:00: 2000000 INFO @ Tue, 16 Jun 2020 09:56:05: 7000000 INFO @ Tue, 16 Jun 2020 09:56:08: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:56:13: 8000000 INFO @ Tue, 16 Jun 2020 09:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:56:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:15: 4000000 INFO @ Tue, 16 Jun 2020 09:56:21: 9000000 INFO @ Tue, 16 Jun 2020 09:56:22: 1000000 INFO @ Tue, 16 Jun 2020 09:56:23: 5000000 INFO @ Tue, 16 Jun 2020 09:56:25: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:56:25: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:56:25: #1 total tags in treatment: 9577974 INFO @ Tue, 16 Jun 2020 09:56:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:56:25: #1 tags after filtering in treatment: 9577974 INFO @ Tue, 16 Jun 2020 09:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:26: #2 number of paired peaks: 1699 INFO @ Tue, 16 Jun 2020 09:56:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:26: #2 predicted fragment length is 193 bps INFO @ Tue, 16 Jun 2020 09:56:26: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 16 Jun 2020 09:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.05_model.r INFO @ Tue, 16 Jun 2020 09:56:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:30: 2000000 INFO @ Tue, 16 Jun 2020 09:56:31: 6000000 INFO @ Tue, 16 Jun 2020 09:56:38: 3000000 INFO @ Tue, 16 Jun 2020 09:56:39: 7000000 INFO @ Tue, 16 Jun 2020 09:56:46: 4000000 INFO @ Tue, 16 Jun 2020 09:56:47: 8000000 INFO @ Tue, 16 Jun 2020 09:56:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:54: 5000000 INFO @ Tue, 16 Jun 2020 09:56:55: 9000000 INFO @ Tue, 16 Jun 2020 09:56:59: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:56:59: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:56:59: #1 total tags in treatment: 9577974 INFO @ Tue, 16 Jun 2020 09:56:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:56:59: #1 tags after filtering in treatment: 9577974 INFO @ Tue, 16 Jun 2020 09:56:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:59: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:57:00: #2 number of paired peaks: 1699 INFO @ Tue, 16 Jun 2020 09:57:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:00: #2 predicted fragment length is 193 bps INFO @ Tue, 16 Jun 2020 09:57:00: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 16 Jun 2020 09:57:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.10_model.r INFO @ Tue, 16 Jun 2020 09:57:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.05_summits.bed INFO @ Tue, 16 Jun 2020 09:57:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3652 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:01: 6000000 INFO @ Tue, 16 Jun 2020 09:57:09: 7000000 INFO @ Tue, 16 Jun 2020 09:57:15: 8000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:57:22: 9000000 INFO @ Tue, 16 Jun 2020 09:57:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:26: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:57:26: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:57:26: #1 total tags in treatment: 9577974 INFO @ Tue, 16 Jun 2020 09:57:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:57:26: #1 tags after filtering in treatment: 9577974 INFO @ Tue, 16 Jun 2020 09:57:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:27: #2 number of paired peaks: 1699 INFO @ Tue, 16 Jun 2020 09:57:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:27: #2 predicted fragment length is 193 bps INFO @ Tue, 16 Jun 2020 09:57:27: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 16 Jun 2020 09:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.20_model.r INFO @ Tue, 16 Jun 2020 09:57:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.10_summits.bed INFO @ Tue, 16 Jun 2020 09:57:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2497 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985666/SRX5985666.20_summits.bed INFO @ Tue, 16 Jun 2020 09:58:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1382 records, 4 fields): 2 millis CompletedMACS2peakCalling